Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

(2019) Gustavo A. Bravo et al.   PeerJ

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Modeling Hybridization Under the Network Multispecies Coalescent

(2018) James H Degnan   SYSTEMATIC BIOLOGY

The Effect of Gene Flow on Coalescent-based Species-Tree Inference

(2018) Colby Long et al.   SYSTEMATIC BIOLOGY

The Biogeography of Deep Time Phylogenetic Reticulation

(2018) Frank T Burbrink et al.   SYSTEMATIC BIOLOGY

HyDe: A Python Package for Genome-Scale Hybridization Detection

(2018) Paul D Blischak et al.   SYSTEMATIC BIOLOGY

Inference of Adaptive Shifts for Multivariate Correlated Traits

(2018) Paul Bastide et al.   SYSTEMATIC BIOLOGY

Inferring Phylogenetic Networks Using PhyloNet

(2018) Dingqiao Wen et al.   SYSTEMATIC BIOLOGY

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

(2018) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods

(2018) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

(2018) Daniel J. Lawson et al.   Nature Communications

Inferring introgression using RADseq and D FOIL : power and pitfalls revealed in a case study of spiny lizards (Sceloporus )

(2018) Shea M. Lambert et al.   Molecular Ecology Resources

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus )

(2018) Christopher Blair et al.   Molecular Ecology Resources

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

(2017) Julien Jouganous et al.   GENETICS

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Networks from Multilocus Sequence Data

(2017) Chi Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

(2017) Dingqiao Wen et al.   SYSTEMATIC BIOLOGY

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

(2017) Julien Jouganous et al.   GENETICS

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

(2016) Hussein A. Hejase et al.   BMC BIOINFORMATICS

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inconsistency of Species Tree Methods under Gene Flow

(2016) Claudia Solís-Lemus et al.   SYSTEMATIC BIOLOGY

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

Fast and accurate detection of evolutionary shifts in Ornstein-Uhlenbeck models

(2016) Mohammad Khabbazian et al.   Methods in Ecology and Evolution

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Reliable ABC model choice via random forests

(2015) Pierre Pudlo et al.   BIOINFORMATICS

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

(2015) Zhenxiang Xi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow

(2012) T. Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Slope heuristics: overview and implementation

(2011) Jean-Patrick Baudry et al.   STATISTICS AND COMPUTING

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Gaussian model selection with an unknown variance

(2009) Yannick Baraud et al.   ANNALS OF STATISTICS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

(2008) A ECKERT et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation

(2008) J. Mallet   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES